CTSG p.Phe176=
c.528C>T · rs145092554 · VCV783685
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.777%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.24 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -4 |
| Overall | ||
| CADD | 5.946 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.777%
African / African-American · 583/75,006 alleles
Filtering AF
0.725%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.704%
Overall
0.0405%
649/1,602,416 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.777% | 129 |
| Admixed American | 0.0467% | 2,143 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,313 |
| South Asian | 0.00329% | 30,357 |
| European (non-Finnish) | 0.000678% | 147,491 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CTSG
- Protein
- p.Phe176=
- Coding
- c.528C>T
- MANE Select
- NM_001911
- dbSNP
- rs145092554
- Type
- single nucleotide variant
- Location
- chr14:24574311 (GRCh38)
- Gene constraint
- LOEUF 1.391 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.89 · 16 PDB
- Residue 176
- a disulfide bond; a β-strand; the peptidase s1 domain
Similar variants
- CTSG p.Asn125Ser Benign ★★ same type
- CTSG p.Gly15Ala Benign ★★ same type
- CTSG p.Thr90Ile Benign ★★ same type
- CTSG p.Arg116Gly Uncertain significance ★ ⚠ same type
- CTSG p.Arg120Gln Uncertain significance ★ ⚠ same type
- CTSG p.Arg153Trp Uncertain significance ★ ⚠ same type
- CTSG p.Arg154Lys Uncertain significance ★ ⚠ same type
- CTSG p.Arg174His Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ctsg-p-phe176 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown